Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

HRX : Summary

Code

HRX

One-letter code

X

Molecule name

[1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid)

Systematic names

ProgramVersionName
ACDLabs 12.01 [1-hydroxy-3-(pyridin-3-yl)propane-1,1-diyl]bis(phosphonic acid)
OpenEye OEToolkits 1.7.6 (1-oxidanyl-1-phosphono-3-pyridin-3-yl-propyl)phosphonic acid

Formula

C8 H13 N O7 P2

Formal charge

0

Molecular weight

297.139 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)C(O)(CCc1cccnc1)P(=O)(O)O
SMILES CACTVS 3.385 OC(CCc1cccnc1)([P](O)(O)=O)[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1cc(cnc1)CCC(O)(P(=O)(O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.385 OC(CCc1cccnc1)([P](O)(O)=O)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(cnc1)CCC(O)(P(=O)(O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C8H13NO7P2/c10-8(17(11,12)13,18(14,15)16)4-3-7-2-1-5-9-6-7/h1-2,5-6,10H,3-4H2,(H2,11,12,13)(H2,14,15,16)

IUPAC InChI key

ILROXFQHACCDLA-UHFFFAOYSA-N
HRX

wwPDB Information

Atom count

31 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-12-10

Last modified at

2015-04-10

Status

Released

Obsoleted

Not Assigned



HRX : Atoms of Molecule

Total Number of Atoms: 31
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O17 O O17 N N N 0 -1.856 -2.826 0.068
2 P14 P P14 N N N 0 -2.202 -1.306 -0.334
3 O16 O O16 N N N 0 -2.095 -1.148 -1.802
4 O15 O O15 N N N 0 -3.701 -0.954 0.136
5 C8 C C8 N N N 0 -1.027 -0.178 0.486
6 P9 P P9 N N N 0 -1.418 1.543 0.03
7 O11 O O11 N N N 0 -1.303 1.715 -1.567
8 O12 O O12 N N N 0 -2.796 1.867 0.462
9 O10 O O10 N N N 0 -0.381 2.539 0.754
10 O13 O O13 N N N 0 -1.13 -0.331 1.903
11 C7 C C7 N N N 0 0.397 -0.513 0.039
12 C9 C C9 N N N 0 1.383 0.433 0.727
13 C6 C C6 N Y N 0 2.786 0.104 0.287
14 C5 C C5 N Y N 0 3.335 0.72 -0.827
15 C2 C C2 N Y N 0 4.63 0.386 -1.195
16 C3 C C3 N Y N 0 5.325 -0.543 -0.444
17 N4 N N4 N Y N 0 4.771 -1.11 0.61
18 C1 C C1 N Y N 0 3.544 -0.812 0.992
19 H1 H H1 N N N 0 -2.443 -3.482 -0.333
20 H2 H H2 N N N 0 -3.844 -1.036 1.089
21 H3 H H3 N N N 0 -0.424 1.519 -1.921
22 H4 H H4 N N N 0 -0.53 3.474 0.556
23 H5 H H5 N N N 0 -0.935 -1.224 2.217
24 H6 H H6 N N N 0 0.631 -1.542 0.311
25 H7 H H7 N N N 0 0.476 -0.396 -1.042
26 H8 H H8 N N N 0 1.149 1.463 0.454
27 H9 H H9 N N N 0 1.305 0.317 1.808
28 H10 H H10 N N N 0 2.768 1.442 -1.395
29 H11 H H11 N N N 0 5.089 0.846 -2.057
30 H12 H H12 N N N 0 6.334 -0.808 -0.724
31 H13 H H13 N N N 0 3.123 -1.297 1.86



HRX : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O12 P9 O P doub 1.48 N N
2 N4 C1 N C doub 1.32 N Y
3 N4 C3 N C sing 1.32 N Y
4 C1 C6 C C sing 1.38 N Y
5 C3 C2 C C doub 1.38 N Y
6 O10 P9 O P sing 1.61 N N
7 P9 O11 P O sing 1.61 N N
8 P9 C8 P C sing 1.82 N N
9 O13 C8 O C sing 1.43 N N
10 C7 C8 C C sing 1.53 N N
11 C7 C9 C C sing 1.53 N N
12 C6 C9 C C sing 1.51 N N
13 C6 C5 C C doub 1.39 N Y
14 C2 C5 C C sing 1.39 N Y
15 C8 P14 C P sing 1.82 N N
16 P14 O16 P O doub 1.48 N N
17 P14 O15 P O sing 1.61 N N
18 P14 O17 P O sing 1.61 N N
19 O17 H1 O H sing 0.97 N N
20 O15 H2 O H sing 0.97 N N
21 O11 H3 O H sing 0.97 N N
22 O10 H4 O H sing 0.97 N N
23 O13 H5 O H sing 0.97 N N
24 C7 H6 C H sing 1.09 N N
25 C7 H7 C H sing 1.09 N N
26 C9 H8 C H sing 1.09 N N
27 C9 H9 C H sing 1.09 N N
28 C5 H10 C H sing 1.08 N N
29 C2 H11 C H sing 1.08 N N
30 C3 H12 C H sing 1.08 N N
31 C1 H13 C H sing 1.08 N N



HRX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
HRX 4rxc Open in New Window Bound ligand 4 1